This proposal studies the mechanisms by which cells respond to DNA damaging agents. A specialized technology developed early in this project will be used to define the relationships among the structures of lesions formed in the genome by carcinogens and the biological endpoints of mutation, cancer and lethality. This proposal addresses our longstanding interest on the genotoxic mechanisms of three classes of agents: simple DNA alkylating agents, a furanocoumarin (aflatoxin) epoxide, and the reactive species associated with inflammation. By studying a carefully chosen range of DNA lesion structures, we seek to understand the strategies used in biology to address the challenge of DNA damage. While the work principally focuses on challenges to cellular DNA repair and DNA replication systems, we also propose here a new dimension to the project through an attempt to understand the challenges faced by damage to RNA nucleotides. Some of our work probes the biochemistry of enzymes that act upon damage in vitro, but the signature element of our program is its focus on using chemistry and genetics to understand in vivo mechanisms. Most of the work begins with the construction of intact viral or plasmid vectors containing, at one genome site, one of the DNA lesions hypothesized to be responsible for mutagenesis or toxicity. Following introduction of the site-specifically modified genome into bacterial or mammalian cells, the genome is replicated either intra- or extra-chromosomally. We have the ability to control exposure to repair enzymes and, to a certain extent, the polymerases that encounter the lesion in vivo. The type, amount and genetic requirements for mutagenesis and lesion lethality are evaluated. By comparison of lethality and mutagenesis in different cell lines, it is possible to determine to what extent specific genetic backgrounds protect, or sensitize, the cell to specific DNA or RNA lesions.

Public Health Relevance

DNA damage can kill cells and, if the cell survives, causes mutations that could engender cancer or other genetic diseases. This proposal uses chemical tools to construct genomes of viruses that contain the DNA lesions, or adducts, formed by carcinogens. The work then progresses to a genetic phase that helps establish rules that predict the types of DNA damage that give rise to the kinds of mutations observed in genetic diseases.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37CA080024-15
Application #
8212351
Study Section
Cancer Etiology Study Section (CE)
Program Officer
Okano, Paul
Project Start
1998-07-01
Project End
2013-02-28
Budget Start
2012-03-01
Budget End
2013-02-28
Support Year
15
Fiscal Year
2012
Total Cost
$393,681
Indirect Cost
$151,181
Name
Massachusetts Institute of Technology
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139
Chawanthayatham, Supawadee; Thiantanawat, Apinya; Egner, Patricia A et al. (2015) Prenatal exposure of mice to the human liver carcinogen aflatoxin B1 reveals a critical window of susceptibility to genetic change. Int J Cancer 136:1254-62
Singh, Vipender; Fedeles, Bogdan I; Essigmann, John M (2015) Role of tautomerism in RNA biochemistry. RNA 21:1-13
Techapiesancharoenkij, Nirachara; Fiala, Jeannette L A; Navasumrit, Panida et al. (2015) Sulforaphane, a cancer chemopreventive agent, induces pathways associated with membrane biosynthesis in response to tissue damage by aflatoxin B1. Toxicol Appl Pharmacol 282:52-60
Fedeles, Bogdan I; Singh, Vipender; Delaney, James C et al. (2015) The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond. J Biol Chem 290:20734-42
Peng, Chunte Sam; Fedeles, Bogdan I; Singh, Vipender et al. (2015) Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity. Proc Natl Acad Sci U S A 112:3229-34
Chang, Shiou-chi; Fedeles, Bogdan I; Wu, Jie et al. (2015) Next-generation sequencing reveals the biological significance of the N(2),3-ethenoguanine lesion in vivo. Nucleic Acids Res 43:5489-500
Fedeles, Bogdan I; Freudenthal, Bret D; Yau, Emily et al. (2015) Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer. Proc Natl Acad Sci U S A 112:E4571-80
Li, Deyu; Fedeles, Bogdan I; Singh, Vipender et al. (2014) Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2'-deoxycytidine. Proc Natl Acad Sci U S A 111:E3252-9
Shrivastav, Nidhi; Fedeles, Bogdan I; Li, Deyu et al. (2014) A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo. PLoS One 9:e94716
Singh, Vipender; Fedeles, Bogdan I; Li, Deyu et al. (2014) Mechanism of repair of acrolein- and malondialdehyde-derived exocyclic guanine adducts by the α-ketoglutarate/Fe(II) dioxygenase AlkB. Chem Res Toxicol 27:1619-31

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